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Fix issues reported from users and prototype manual reduction #41

Merged
merged 114 commits into from
Apr 26, 2019
Merged

Fix issues reported from users and prototype manual reduction #41

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3d507f0
Refs #38. Minor changes at strain/stress UI.
wdzhou Oct 29, 2018
9ebd37a
Refs #40. Enable peak fit (core) to calculate center in dspace after …
wdzhou Oct 30, 2018
c1a7a03
Refs #38. Made 1D slice work.
wdzhou Oct 31, 2018
67c8c81
Refs #38. Caught an except for a non-existing direciton E33.
wdzhou Oct 31, 2018
c313cff
Refs #39. Tried to fix auto scale with plot.
wdzhou Nov 1, 2018
daf7f5e
Refs #42 and #43 and #44. Initialize pole figure with NaN and.
wdzhou Nov 5, 2018
6d671c7
Refs #42. Fixed an error if pole figure contour is init to nan.
wdzhou Nov 5, 2018
60c42e7
Refs #32. Checkpointing some progress.
wdzhou Nov 14, 2018
69602ed
Refs #32. Checkpointing progress in implementing data reduction engine.
wdzhou Nov 16, 2018
b578373
Refs #32. Added a test file for reduction.
wdzhou Nov 19, 2018
06778f6
Refs #47 and #48. Improved UI for separate fit result window.
wdzhou Nov 19, 2018
c8e0973
Refs #47 and #32. Added auto reduction script and new mpl widgets.
wdzhou Nov 21, 2018
ec9796a
Refs #32. Fixed many issues of the data/model and residual plot widget.
wdzhou Nov 22, 2018
3f2e2e6
Refs #32. Enabled synchronization of zoom operation on 2 subplots.
wdzhou Nov 26, 2018
4ef20d8
Refs #45. Checkpointing progress to implement calibration information…
wdzhou Dec 1, 2018
27ae144
Refs #45. Checkpointing progress on implementing calibration manager.
wdzhou Dec 4, 2018
f9eed8e
Re-organize the prototyp scripts.
wdzhou Dec 4, 2018
82d1174
Refs #32 and #36. Changed the MTEX's posfix to jul.
wdzhou Dec 4, 2018
da41b4f
Refs #32 and #36. Fixed MTEX header issue and progress in reduction.
wdzhou Dec 5, 2018
788f5cc
Refs #40 and #48. Set up the fitting result table dynamically.
wdzhou Dec 5, 2018
b29547f
Refs #32. Continuing to modify peak fitting result table.
wdzhou Dec 6, 2018
ee359ac
Refs #45. Created class for calibrated geometry parameters.
wdzhou Dec 7, 2018
012dd64
Refs #32. Added test data.
wdzhou Dec 14, 2018
d161732
Merge branch 'prototype_manual_reduction_032' of github.com:neutrons/…
wdzhou Dec 14, 2018
ce3d75d
Refs #32. Removed a prototpye.
wdzhou Dec 14, 2018
11baa89
Refs #32. Refactored reduction UI and added IPython console.
wdzhou Dec 18, 2018
3748b5e
Refs 32. Added reduction prototype and modifed reduction UI.
wdzhou Dec 18, 2018
a383d34
Refs #32. Added prototype files.
wdzhou Dec 19, 2018
0135dfa
Refs #32. Added 2 ipython scripts for building instrument.
wdzhou Dec 28, 2018
4cf0641
Refs #32. Added a pure python HB2B reduction prototype.
wdzhou Jan 1, 2019
0bd4ce8
Refs #32. Some progress on creating HB2B.
wdzhou Jan 2, 2019
fb999ee
Refs #32. Added test cases for HB2B builder.
wdzhou Jan 3, 2019
355dd71
Refs #32. Checkpointing progress on HB2B reduction.
wdzhou Jan 3, 2019
ae136c3
Refs #32. Added test cases for instrument builder.
wdzhou Jan 4, 2019
250d17a
Refs #32. Fixed some issues with HB2B builder.
wdzhou Jan 4, 2019
d80f9f2
Refs #32. Added test data.
wdzhou Jan 4, 2019
e439f75
Refs #32. Updated reduce x ray data script.
wdzhou Jan 4, 2019
2c5ebbd
Refs #32. Add an updated UI.
wdzhou Jan 4, 2019
ba62b90
Refs #32. Added geometry and reduction test scripts and data.
wdzhou Jan 7, 2019
7c9e6e5
Refs #32. Added a zero degree mask file.
wdzhou Jan 7, 2019
f447a7f
Refs #32. Added 2 more testing binary data set.
wdzhou Jan 7, 2019
4653170
Refs #32. Checkpointing progress to implement reduction and test script.
wdzhou Jan 8, 2019
7e27667
Refs #32. Fixed some issues with reduction with PyRS/no-mantid.
wdzhou Jan 8, 2019
d7daaff
Refs #32. Added reduction script.
wdzhou Jan 9, 2019
8524847
Refs #32. Checkpointing progress on masking for calibration.
wdzhou Jan 9, 2019
748dab4
Refs #32. Checkpointing progress on reduction prototype.
wdzhou Jan 10, 2019
b5645d5
#32. Started to build the calibration and reduction framework.
wdzhou Jan 16, 2019
13a2d06
Refs #32. Updated manually corrected X-ray IDF.
wdzhou Jan 16, 2019
d319260
Refs #32. Corrected geometry error from both PyRS and Mantid IDF.
wdzhou Jan 17, 2019
386cc7b
Refs #32. Corrected HB2B IDF finally.
wdzhou Jan 17, 2019
50183d0
Refs #32. More work on reduction and reduction with mask.
wdzhou Jan 18, 2019
7ae2e23
Refs #32. Started to implement script to reduce X-ray data and manipu…
wdzhou Jan 25, 2019
9b11b0a
Refs #32. Checkpointing progress to refactor the code organization.
wdzhou Jan 25, 2019
58a4709
Refs #32. Checkpointing progress to refactor the code organization (2).
wdzhou Jan 25, 2019
3dddce5
Refs #32. Set up unit tests with reduction.
wdzhou Jan 25, 2019
6d2b529
Refs #32. Checkpointing progress on masking.
wdzhou Jan 28, 2019
ad26c5b
Refs #32. Checkpointing progress to implement reduction script and ma…
wdzhou Jan 30, 2019
6f52f9d
Refs #32. Resolved issues observed during testing mask processing.
wdzhou Jan 30, 2019
364af05
Refs #32. Checkpointing progress on reduction script.
wdzhou Jan 31, 2019
99dee3c
Refs #32. Checkpointing progress on reduction script and modified cal…
wdzhou Feb 1, 2019
99fd126
Refs #32. Checkpointing progress on reduction with mask.
wdzhou Feb 1, 2019
5a76dcb
Refs #49 and #32. Improved calibration UI and reduction script.
wdzhou Feb 1, 2019
d7df233
Refs #32 and #49. Checkpointing progress on calibration UI and reduct…
wdzhou Feb 5, 2019
ed65388
Refs #49. Added calibration GUI test and fixed some issues.
wdzhou Feb 5, 2019
c90d720
Refs #32. Checkpoing progress on implementing reduction engine and sc…
wdzhou Feb 5, 2019
556babe
Refs #49. Checkpointing progress on calibration GUI.
wdzhou Feb 6, 2019
d938363
Refs #49. Added extended graphics view to calibration window.
wdzhou Feb 6, 2019
feabd49
Refs #32 and #49. Checkpointing progress on calibration UI.
wdzhou Feb 7, 2019
e8e7127
Refs #32. Solved some issues for reduction script testing.
wdzhou Feb 7, 2019
6f5cc2e
Refs #32. Added 2theta range options to reduction script and methods.
wdzhou Feb 8, 2019
0cc24f2
Refs #32. Corrected some workflow issue.
wdzhou Feb 8, 2019
460ea04
Refs #32. Solved an issue of reduction: np.histogram takes np.int32 b…
wdzhou Feb 8, 2019
28a9e95
Refs #32. Fixed some issues with reduction script with mantid engine.
wdzhou Feb 11, 2019
ec50991
Refs #32. Added a unit test to verify algorithsm to build instrument.
wdzhou Feb 12, 2019
1bc5d52
Refs #32. Added unit test of arbitrary detector position test.
wdzhou Feb 14, 2019
a673a67
Refs 49. Checkpointing improvement on calibration interface.
wdzhou Feb 14, 2019
e260df0
Refs #32 and #49. Finished the unit tests for reduction and progress …
wdzhou Feb 19, 2019
a376d95
Refs #32. Fixed some issues about reducing data in calibration window.
wdzhou Feb 22, 2019
e74951c
Refs #32 and #49. Checked Mantid and pyrs comparison test to (5) and …
wdzhou Mar 7, 2019
a6e98fe
Refs #32 and #49. Checkpointing progress on reduction unit test and c…
wdzhou Mar 8, 2019
bc1a1f0
Refs #32 amd #49. Implemented tiff/bin to HDF convert script.
wdzhou Mar 11, 2019
220a779
Refs #32. Checkpointing progress.
wdzhou Mar 20, 2019
fa8eb05
Refs #32. Checkpointing improvements on command and testing script.
wdzhou Mar 21, 2019
f79ed8a
Refs #32. Fixed issues to make convert_raw_data to pass and etc.
wdzhou Mar 21, 2019
9f58b0b
Refs #32. Fixed issues with creating masks from Mantid XML (not
wdzhou Mar 22, 2019
902e9be
Refs #32. Passed masking test.
wdzhou Mar 22, 2019
001edb5
Refs #32. Checkpointing progress on geometry comparison.
wdzhou Mar 22, 2019
a94a6c2
Refs #32. Fixed an issue to pass verify_pyrs_reduction 1.
wdzhou Mar 25, 2019
0612bb9
Refs #32. Checkpointing progress to implement an instrument class.
wdzhou Mar 26, 2019
32f3767
Refs #32. Checkpointing progress to implement PyRS instrument class.
wdzhou Apr 2, 2019
ebf2a04
Refs #32. Checkpointing progress in converting to 2theta comparison.
wdzhou Apr 3, 2019
a0580f7
Refs #32. Fixed the issue to convert to 2theta by Mantid.
wdzhou Apr 3, 2019
bf04989
Refs #32. Tried to compare pixel by pixel for position.
wdzhou Apr 3, 2019
255ab6a
Refs #32. fixed a bug.
wdzhou Apr 3, 2019
e4808e0
Refs #32. Find out the source of discrepancy: resolution of calibrate…
wdzhou Apr 4, 2019
425394d
Refs #32. Checkpointing progress to compare reduction result.
wdzhou Apr 5, 2019
3f2b867
Refs #32. Disabled to outputs.
wdzhou Apr 5, 2019
11c16dc
Refs #32. Implemented a simple histogram method for comparison check.
wdzhou Apr 11, 2019
90a27cc
Refs #32. Used numpy histogram for Mantid reduction.
wdzhou Apr 11, 2019
d2b41c3
Refs #32. Checkpointing progress to testing reducing to 2theta.
wdzhou Apr 12, 2019
81ce1e7
Refs #72. The reduced value diffrence may come from different 2theta …
wdzhou Apr 12, 2019
53f9a9d
Refs #32. Passed no mask reduction.
wdzhou Apr 12, 2019
0ea4abf
Refs #32. Passed 0 and 10 degree mask test.
wdzhou Apr 12, 2019
dd02c59
Refs #32. Added normalization to mantid one.
wdzhou Apr 16, 2019
863716b
Refs #32. Added normalization for mantid.
wdzhou Apr 16, 2019
29ccc46
Refs #32. Added another testing script for using PyRS only.
wdzhou Apr 16, 2019
6c13b90
Refs #32. Complete a new script to study the binning.
wdzhou Apr 18, 2019
4c69c27
Refs #32. Refactored PyRS instrument builder.
wdzhou Apr 21, 2019
f7c6c85
Refs #32. Implemented SortXAxis/ResampleX approach.
wdzhou Apr 21, 2019
b19b2ba
Refs #32. Resolved the conflict.
wdzhou Apr 21, 2019
8b61c04
Refs #32. Implemented reduction script.
wdzhou Apr 26, 2019
640801a
Refs #32. Checkpointing progress.
wdzhou Apr 26, 2019
619766f
Refs #32. Fixed a plot issue.
wdzhou Apr 26, 2019
edf96fd
Refs #32. Final commit on this long (time) PR with minor change.
wdzhou Apr 26, 2019
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9 changes: 9 additions & 0 deletions create_calibration_masks.sh
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sh pyrs_command.sh 1 --roi=tests/testdata/masks/NegZ_Mask.xml --output=tests/testdata/masks/NegZ.hdf5 --note=ROI_NegZ
sh pyrs_command.sh 1 --roi=tests/testdata/masks/NegZ_Mask.xml --output=tests/testdata/masks/PosZ.hdf5 --note=ROI_PosZ --operation=reverse
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_0_Mask.xml --opeation=reverse --output=tests/testdata/masks/Chi_0.hdf5 --note=35_Degree_SolidAngle_0
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_10_Mask.xml --roi=tests/testdata/masks/PosZ.hdf5 --operation=and --output=tests/testdata/masks/Chi_10.hdf5 --note=35_Degree_SolidAngle_Pos10
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_10_Mask.xml --roi=tests/testdata/masks/NegZ.hdf5 --operation=and --output=tests/testdata/masks/Chi_Neg10.hdf5 --note=35_Degree_SolidAngle_Neg10
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_20_Mask.xml --roi=tests/testdata/masks/PosZ.hdf5 --operation=and --output=tests/testdata/masks/Chi_20.hdf5 --note=35_Degree_SolidAngle_Pos20
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_20_Mask.xml --roi=tests/testdata/masks/NegZ.hdf5 --operation=and --output=tests/testdata/masks/Chi_Neg20.hdf5 --note=35_Degree_SolidAngle_Neg20
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_30_Mask.xml --roi=tests/testdata/masks/PosZ.hdf5 --operation=and --output=tests/testdata/masks/Chi_30.hdf5 --note=35_Degree_SolidAngle_Pos30
sh pyrs_command.sh 1 --roi=tests/testdata/masks/Chi_30_Mask.xml --roi=tests/testdata/masks/NegZ.hdf5 --operation=and --output=tests/testdata/masks/Chi_Neg30.hdf5 --note=35_Degree_SolidAngle_Neg30
266 changes: 266 additions & 0 deletions designer/WorkspacesView.ui
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<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>Form</class>
<widget class="QWidget" name="Form">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>1437</width>
<height>895</height>
</rect>
</property>
<property name="windowTitle">
<string>Form</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
<widget class="QGroupBox" name="groupBox_upperRight">
<property name="title">
<string>Logs</string>
</property>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<widget class="QDockWidget" name="dockWidget_wsList">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="acceptDrops">
<bool>true</bool>
</property>
<property name="floating">
<bool>false</bool>
</property>
<widget class="QWidget" name="dockWidgetContents_5">
<layout class="QGridLayout" name="gridLayout_4">
<item row="0" column="0">
<widget class="QTabWidget" name="tabWidget_logging">
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="tab_3">
<attribute name="title">
<string>Latest</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_8">
<item row="0" column="0">
<widget class="QPlainTextEdit" name="plainTextEdit_info"/>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab_error">
<attribute name="title">
<string>Error</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_9">
<item row="0" column="0">
<widget class="QPlainTextEdit" name="plainTextEdit_error"/>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab_4">
<attribute name="title">
<string>History</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_7">
<item row="0" column="0">
<widget class="QPlainTextEdit" name="plainTextEdit_loggingHistory"/>
</item>
</layout>
</widget>
</widget>
</item>
</layout>
</widget>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupBox_4">
<property name="title">
<string>Workspaces and Simple Visualization</string>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<item row="0" column="0">
<widget class="QDockWidget" name="dockWidget_graphic">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="acceptDrops">
<bool>true</bool>
</property>
<property name="floating">
<bool>false</bool>
</property>
<widget class="QWidget" name="dockWidgetContents_4">
<layout class="QGridLayout" name="gridLayout_5">
<item row="0" column="0">
<widget class="QTabWidget" name="tabWidget_table_view">
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="tab">
<attribute name="title">
<string>Workspaces</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_6">
<item row="0" column="0">
<widget class="QFrame" name="frame_tableWidget_dataStructure">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
</widget>
</item>
<item row="0" column="1">
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
<widget class="QPushButton" name="pushButton_toIPython">
<property name="text">
<string>To IPython (Name)</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_toIPythonMtd">
<property name="text">
<string>To IPython (mtd)</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_toIPythonAssign">
<property name="text">
<string>To IPython (assign)</string>
</property>
</widget>
</item>
<item>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
</layout>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab_2">
<attribute name="title">
<string>Plot Data</string>
</attribute>
<layout class="QVBoxLayout" name="verticalLayout_3">
<item>
<widget class="QFrame" name="frame_graphicsView_general">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>600</width>
<height>0</height>
</size>
</property>
<property name="acceptDrops">
<bool>false</bool>
</property>
<property name="autoFillBackground">
<bool>true</bool>
</property>
<property name="interactive" stdset="0">
<bool>false</bool>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QPushButton" name="pushButton_fitCanvas">
<property name="text">
<string>Fit Canvas</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_clear">
<property name="toolTip">
<string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Clear image on the right&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
<property name="text">
<string>Clear</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</widget>
</item>
</layout>
</widget>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QGroupBox" name="groupBox_2">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>320</height>
</size>
</property>
<property name="title">
<string>iPython Console</string>
</property>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0">
<widget class="QFrame" name="frame_widget_ipython">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<resources/>
<connections/>
</ui>
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